Aside from installing and removing programs, DLL share problems will show up in a registry cleaning check for a number of reasons.
My first question would be what software (and version) are you using for registry cleaning?
None of the registry cleaners I have tried are perfect.
They all miss some problems and detect good keys as bad.
Just the process of running a program that created the shared DLL key that your registry cleaner detects as bad could re-create the key.
Some keys that show up as bad in a registry clean are simply bad because the program uses that key along with a temporary file that is removed when you close the program.
As far as securing your system, the first step is a good software firewall.
Even if you only have a dial-up connection to the Internet, a firewall is now a must have.
There are a number of good choices out there. The one recommended most often by peers here at TR is Zone Alarm from www.zonelabs.com
If this is a business network, a good hardware firewall is a must.
Next, assuming your drives are formatted as NTFS volumes, you can enable security on selected files and folders.
Open Windows Explorer.
Browse to the folder or file you wish to secure.
Right click on the file or folder and select sharing and security options.
Set the security options as needed.
Chas